Major technical advances were introduced in the study of microflora and microbial communities in the nineties. These are essentially analytical approaches conducted as frequently by brute force. What conclusions can be drawn from these analyses twenty years later? In terms of microbial compositions, monitoring and diagnosis, the results are impressive. But what do all these microorganisms do? What are the factors behind their associations and their maintenance? Gene inventories are approaching completion; they allow us to deepen some physiological processes but do not say much more. We have even begun to manipulate microbiota. But as often in the dialectic between theory and practice, it works but we are far from understanding how!